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lammps/src/SMTBQ/pair_smatb_single.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Daniele Rapetti (iximiel@gmail.com)
------------------------------------------------------------------------- */
#include "pair_smatb_single.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairSMATBSingle::PairSMATBSingle(LAMMPS *_lmp) :
Pair(_lmp), nmax(0), on_eb(nullptr), r0(0), p(0), A(0), q(0), QSI(0), cutOffStart(0),
cutOffEnd(0), cutOffEnd2(0), a3(0), a4(0), a5(0), x3(0), x4(0), x5(0)
{
single_enable = 0; // 1 if single() routine exists
restartinfo = 1; // 1 if pair style writes restart info
respa_enable = 0; // 1 if inner/middle/outer rRESPA routines
one_coeff = 0; // 1 if allows only one coeff * * call
manybody_flag = 1; // 1 if a manybody potential
no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute()
writedata = 1; // 1 if writes coeffs to data file
ghostneigh = 0; // 1 if pair style needs neighbors of ghosts
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
PairSMATBSingle::~PairSMATBSingle()
{
if (copymode) { return; }
memory->destroy(on_eb);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::compute(int eflag, int vflag)
{
int i, j, ii, jj, jnum;
double xtmp, ytmp, ztmp, del[3], fpair;
double dijsq, dij;
double espo, aexpp, qsiexpq, eb_i, Fb, Fr;
double polyval, polyval2, polyval3, polyval4, polyval5;
if (eflag || vflag) {
ev_setup(eflag, vflag);
eng_vdwl = 0;
} else {
evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
}
// grow on_eb array if necessary
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->grow(on_eb, nmax, "pair_smatb:on_eb");
}
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
// zero out on_eb
if (newton_pair) {
memset(on_eb, 0, nall * sizeof(on_eb[0]));
} else {
memset(on_eb, 0, nlocal * sizeof(on_eb[0]));
}
int inum = list->inum;
int *ilist = list->ilist;
int *jlist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// FIRST LOOP: CALCULATES the squared bonding energy and accumulate it in on_eb for each atom
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; ++jj) {
j = jlist[jj];
j &= NEIGHMASK;
del[0] = xtmp - x[j][0];
del[1] = ytmp - x[j][1];
del[2] = ztmp - x[j][2];
dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2];
if (dijsq < cutOffEnd2) {
dij = sqrt(dijsq);
if (dij < cutOffStart) {
qsiexpq = (QSI * QSI) * exp(2.0 * q * (1.0 - dij / r0));
} else {
polyval = dij - cutOffEnd;
polyval3 = polyval * polyval * polyval;
polyval4 = polyval3 * polyval;
polyval5 = polyval4 * polyval;
qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3;
qsiexpq = qsiexpq * qsiexpq;
}
on_eb[i] += qsiexpq;
on_eb[j] += qsiexpq;
}
}
}
// communicate the squared bonding energy between the various bins
comm->reverse_comm(this);
// Support Loop: take the square root of the bonding energy and
// accumulate it in the energy accumulator if needed the store the
// reciprocal in on_eb in order to not do it in the SECOND LOOP
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
if (i < nlocal) {
eb_i = sqrt(on_eb[i]);
if (eb_i != 0.0) {
on_eb[i] = 1.0 / eb_i;
} else {
on_eb[i] = 0.0;
}
//if needed the bonding energy is accumulated:
if (eflag_either) {
if (eflag_atom) { eatom[i] -= eb_i; }
if (eflag_global) { eng_vdwl -= eb_i; }
}
}
}
// this communication stores the denominators in the ghosts atoms,
// this is needed because of how forces are calculated
comm->forward_comm(this);
// SECOND LOOP: given on_eb[i] calculates forces and energies
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
del[0] = xtmp - x[j][0];
del[1] = ytmp - x[j][1];
del[2] = ztmp - x[j][2];
dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2];
if (dijsq < cutOffEnd2) {
dij = sqrt(dijsq);
if (dij < cutOffStart) {
espo = 1.0 - dij / r0;
aexpp = exp(p * espo) * A;
Fr = (2.0 * aexpp) * (p / r0);
qsiexpq = (QSI * QSI) * exp(2.0 * q * espo);
Fb = -qsiexpq * q / r0;
} else {
polyval = dij - cutOffEnd;
polyval2 = polyval * polyval;
polyval3 = polyval2 * polyval;
polyval4 = polyval3 * polyval;
polyval5 = polyval4 * polyval;
aexpp = a5 * polyval5 + a4 * polyval4 + a3 * polyval3;
Fr = -2.0 * (5.0 * a5 * polyval4 + 4.0 * a4 * polyval3 + 3.0 * a3 * polyval2);
qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3;
Fb = ((5.0 * x5 * polyval4 + 4.0 * x4 * polyval3 + 3.0 * x3 * polyval2)) * qsiexpq;
}
// if needed the repulsive energy is accumulated:
if (eflag_either) {
if (eflag_atom) {
eatom[i] += aexpp;
if (newton_pair || j < nlocal) { eatom[j] += aexpp; }
}
if (eflag_global) {
if (newton_pair || j < nlocal) {
eng_vdwl += 2.0 * (aexpp);
} else {
eng_vdwl += aexpp;
}
}
}
// calculates the module of the pair energy between i and j
fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij;
f[i][0] += del[0] * fpair;
f[i][1] += del[1] * fpair;
f[i][2] += del[2] * fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= del[0] * fpair;
f[j][1] -= del[1] * fpair;
f[j][2] -= del[2] * fpair;
}
if (vflag_atom) {
ev_tally(i, j, nlocal, newton_pair, 0.0,
0.0, //Energy is tally'd in the other parts of the potential
fpair, del[0], del[1], del[2]);
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSMATBSingle::settings(int narg, char **)
{
if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options");
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairSMATBSingle::allocate()
{
int n = atom->ntypes;
int natoms = atom->natoms;
memory->create(setflag, n + 1, n + 1, "pair_smatb:setflag");
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) { setflag[i][j] = 0; }
}
memory->create(cutsq, n + 1, n + 1, "pair_smatb:cutsq");
allocated = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairSMATBSingle::coeff(int narg, char **arg)
{
if (!allocated) { allocate(); }
if (narg != 9) utils::missing_cmd_args(FLERR, "pair_style smatb/single", error);
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
r0 = utils::numeric(FLERR, arg[2], false, lmp);
p = utils::numeric(FLERR, arg[3], false, lmp);
q = utils::numeric(FLERR, arg[4], false, lmp);
A = utils::numeric(FLERR, arg[5], false, lmp);
QSI = utils::numeric(FLERR, arg[6], false, lmp);
cutOffStart = utils::numeric(FLERR, arg[7], false, lmp);
cutOffEnd = utils::numeric(FLERR, arg[8], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairSMATBSingle::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
//calculating the polynomial linking to zero
double es = cutOffEnd - cutOffStart;
double es2 = es * es;
double es3 = es2 * es;
//variables for poly for p and A
double expp = A * exp(p * (1. - cutOffStart / r0));
double ap = -1. / es3;
double bp = p / (r0 * es2);
double cp = -(p * p) / (es * r0 * r0);
a5 = expp * (12. * ap + 6. * bp + cp) / (2. * es2);
a4 = expp * (15. * ap + 7. * bp + cp) / es;
a3 = expp * (20. * ap + 8. * bp + cp) / 2.;
//variables for poly for q and qsi
double expq = QSI * exp(q * (1. - cutOffStart / r0));
double aq = -1 / es3;
double bq = q / (es2 * r0);
double cq = -(q * q) / (es * r0 * r0);
x5 = expq * (12. * aq + 6. * bq + cq) / (2. * es2);
x4 = expq * (15. * aq + 7. * bq + cq) / es;
x3 = expq * (20. * aq + 8. * bq + cq) / 2.;
cutOffEnd2 = cutOffEnd * cutOffEnd;
if (i != j) {
setflag[j][i] = 1;
cutOffEnd2 = cutOffEnd2;
r0 = r0;
p = p;
q = q;
A = A;
QSI = QSI;
cutOffStart = cutOffStart;
cutOffEnd = cutOffEnd;
a3 = a3;
a4 = a4;
a5 = a5;
x3 = x3;
x4 = x4;
x5 = x5;
}
return cutOffEnd;
}
/* ---------------------------------------------------------------------- */
int PairSMATBSingle::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i, j, m;
m = 0;
for (i = 0; i < n; ++i) {
j = list[i];
buf[m++] = on_eb[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::unpack_forward_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; ++i) { on_eb[i] = buf[m++]; }
}
/* ---------------------------------------------------------------------- */
int PairSMATBSingle::pack_reverse_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; ++i) { buf[m++] = on_eb[i]; }
return m;
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::unpack_reverse_comm(int n, int *list, double *buf)
{
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
on_eb[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
//write binary data of this simulation:
void PairSMATBSingle::write_restart_settings(FILE *fp)
{
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
fwrite(&tail_flag, sizeof(int), 1, fp);
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::read_restart_settings(FILE *fp)
{
int me = comm->me;
size_t result;
if (me == 0) {
result = fread(&offset_flag, sizeof(int), 1, fp);
result = fread(&mix_flag, sizeof(int), 1, fp);
result = fread(&tail_flag, sizeof(int), 1, fp);
}
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world);
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i, j;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) {
fwrite(&r0, sizeof(double), 1, fp);
fwrite(&p, sizeof(double), 1, fp);
fwrite(&q, sizeof(double), 1, fp);
fwrite(&A, sizeof(double), 1, fp);
fwrite(&QSI, sizeof(double), 1, fp);
fwrite(&cutOffStart, sizeof(double), 1, fp);
fwrite(&cutOffEnd, sizeof(double), 1, fp);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
size_t result;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); }
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR, &r0, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &p, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &q, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &A, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &QSI, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cutOffStart, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cutOffEnd, sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&r0, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&p, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&q, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&A, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&QSI, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cutOffStart, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cutOffEnd, 1, MPI_DOUBLE, 0, world);
}
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++) {
fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0, p, q, A, QSI, cutOffStart, cutOffEnd);
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
fprintf(fp, "%d %d %g %g %g %g %g %g %g\n", i, j, r0, p, q, A, QSI, cutOffStart, cutOffEnd);
}
}
}
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